| 1 |  | /* | 
| 2 | < | File autogenerated by gengetopt version 2.11 | 
| 2 | > | File autogenerated by gengetopt version 2.22 | 
| 3 |  | generated with the following command: | 
| 4 | < | /home/maul/gezelter/tim/bin/gengetopt -i StaticProps.ggo -F StaticPropsCmd | 
| 4 | > | gengetopt -F StaticPropsCmd -u | 
| 5 |  |  | 
| 6 |  | The developers of gengetopt consider the fixed text that goes in all | 
| 7 |  | gengetopt output files to be in the public domain: | 
| 8 |  | we make no copyright claims on it. | 
| 9 |  | */ | 
| 10 |  |  | 
| 11 | – |  | 
| 12 | – | #include <stdio.h> | 
| 13 | – | #include <stdlib.h> | 
| 14 | – | #include <string.h> | 
| 15 | – |  | 
| 11 |  | /* If we use autoconf.  */ | 
| 12 |  | #ifdef HAVE_CONFIG_H | 
| 13 |  | #include "config.h" | 
| 14 |  | #endif | 
| 15 |  |  | 
| 16 | + | #include <stdio.h> | 
| 17 | + | #include <stdlib.h> | 
| 18 | + | #include <string.h> | 
| 19 | + |  | 
| 20 |  | #include "getopt.h" | 
| 21 |  |  | 
| 22 |  | #include "StaticPropsCmd.h" | 
| 23 |  |  | 
| 24 | + | const char *gengetopt_args_info_purpose = ""; | 
| 25 | + |  | 
| 26 | + | const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]..."; | 
| 27 | + |  | 
| 28 | + | const char *gengetopt_args_info_description = ""; | 
| 29 | + |  | 
| 30 | + | const char *gengetopt_args_info_help[] = { | 
| 31 | + | "  -h, --help                    Print help and exit", | 
| 32 | + | "  -V, --version                 Print version and exit", | 
| 33 | + | "  -i, --input=filename          input dump file", | 
| 34 | + | "  -o, --output=filename         output file name", | 
| 35 | + | "  -n, --step=INT                process every n frame  (default=`1')", | 
| 36 | + | "  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')", | 
| 37 | + | "  -x, --nbins_x=INT             number of bins in x axis  (default=`100')", | 
| 38 | + | "  -y, --nbins_y=INT             number of bins in y axis  (default=`100')", | 
| 39 | + | "      --nbins_z=INT             number of bins in z axis  (default=`100')", | 
| 40 | + | "  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')", | 
| 41 | + | "      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)", | 
| 42 | + | "  -c, --rcut=DOUBLE             cutoff radius (rcut)", | 
| 43 | + | "  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')", | 
| 44 | + | "      --sele1=selection script  select the first stuntdouble set", | 
| 45 | + | "      --sele2=selection script  select the second stuntdouble set", | 
| 46 | + | "      --sele3=selection script  select the third stuntdouble set", | 
| 47 | + | "      --refsele=selection script\n                                select reference (use and only use with --gxyz)", | 
| 48 | + | "      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point", | 
| 49 | + | "      --molname=STRING          molecule name", | 
| 50 | + | "      --begin=INT               begin internal index", | 
| 51 | + | "      --end=INT                 end internal index", | 
| 52 | + | "      --radius=DOUBLE           nanoparticle radius", | 
| 53 | + | "\n Group: staticProps\n   an option of this group is required", | 
| 54 | + | "      --bo                      bond order parameter (--rcut must be specified)", | 
| 55 | + | "      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)", | 
| 56 | + | "      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)", | 
| 57 | + | "  -g, --gofr                    g(r)", | 
| 58 | + | "      --gofz                    g(z)", | 
| 59 | + | "      --r_theta                 g(r, cos(theta))", | 
| 60 | + | "      --r_omega                 g(r, cos(omega))", | 
| 61 | + | "      --r_z                     g(r, z)", | 
| 62 | + | "      --theta_omega             g(cos(theta), cos(omega))", | 
| 63 | + | "      --gxyz                    g(x, y, z)", | 
| 64 | + | "  -p, --p2                      p2 order parameter (--sele1 and --sele2 must be \n                                  specified)", | 
| 65 | + | "      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)", | 
| 66 | + | "  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)", | 
| 67 | + | "  -d, --density                 density plot", | 
| 68 | + | "      --slab_density            slab density", | 
| 69 | + | "      --p_angle                 p(cos(theta))", | 
| 70 | + | "      --hxy                     hxy", | 
| 71 | + | "      --rho_r                   rho of R", | 
| 72 | + | "      --hullvol                 hull volume of nanoparticle", | 
| 73 | + | 0 | 
| 74 | + | }; | 
| 75 | + |  | 
| 76 | + | typedef enum {ARG_NO | 
| 77 | + | , ARG_STRING | 
| 78 | + | , ARG_INT | 
| 79 | + | , ARG_DOUBLE | 
| 80 | + | } cmdline_parser_arg_type; | 
| 81 | + |  | 
| 82 | + | static | 
| 83 | + | void clear_given (struct gengetopt_args_info *args_info); | 
| 84 | + | static | 
| 85 | + | void clear_args (struct gengetopt_args_info *args_info); | 
| 86 | + |  | 
| 87 | + | static int | 
| 88 | + | cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, | 
| 89 | + | struct cmdline_parser_params *params, const char *additional_error); | 
| 90 | + |  | 
| 91 | + | static int | 
| 92 | + | cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error); | 
| 93 | + |  | 
| 94 | + | static char * | 
| 95 | + | gengetopt_strdup (const char *s); | 
| 96 | + |  | 
| 97 | + | static | 
| 98 | + | void clear_given (struct gengetopt_args_info *args_info) | 
| 99 | + | { | 
| 100 | + | args_info->help_given = 0 ; | 
| 101 | + | args_info->version_given = 0 ; | 
| 102 | + | args_info->input_given = 0 ; | 
| 103 | + | args_info->output_given = 0 ; | 
| 104 | + | args_info->step_given = 0 ; | 
| 105 | + | args_info->nbins_given = 0 ; | 
| 106 | + | args_info->nbins_x_given = 0 ; | 
| 107 | + | args_info->nbins_y_given = 0 ; | 
| 108 | + | args_info->nbins_z_given = 0 ; | 
| 109 | + | args_info->nanglebins_given = 0 ; | 
| 110 | + | args_info->length_given = 0 ; | 
| 111 | + | args_info->rcut_given = 0 ; | 
| 112 | + | args_info->zoffset_given = 0 ; | 
| 113 | + | args_info->sele1_given = 0 ; | 
| 114 | + | args_info->sele2_given = 0 ; | 
| 115 | + | args_info->sele3_given = 0 ; | 
| 116 | + | args_info->refsele_given = 0 ; | 
| 117 | + | args_info->comsele_given = 0 ; | 
| 118 | + | args_info->molname_given = 0 ; | 
| 119 | + | args_info->begin_given = 0 ; | 
| 120 | + | args_info->end_given = 0 ; | 
| 121 | + | args_info->radius_given = 0 ; | 
| 122 | + | args_info->bo_given = 0 ; | 
| 123 | + | args_info->bor_given = 0 ; | 
| 124 | + | args_info->bad_given = 0 ; | 
| 125 | + | args_info->gofr_given = 0 ; | 
| 126 | + | args_info->gofz_given = 0 ; | 
| 127 | + | args_info->r_theta_given = 0 ; | 
| 128 | + | args_info->r_omega_given = 0 ; | 
| 129 | + | args_info->r_z_given = 0 ; | 
| 130 | + | args_info->theta_omega_given = 0 ; | 
| 131 | + | args_info->gxyz_given = 0 ; | 
| 132 | + | args_info->p2_given = 0 ; | 
| 133 | + | args_info->rp2_given = 0 ; | 
| 134 | + | args_info->scd_given = 0 ; | 
| 135 | + | args_info->density_given = 0 ; | 
| 136 | + | args_info->slab_density_given = 0 ; | 
| 137 | + | args_info->p_angle_given = 0 ; | 
| 138 | + | args_info->hxy_given = 0 ; | 
| 139 | + | args_info->rho_r_given = 0 ; | 
| 140 | + | args_info->hullvol_given = 0 ; | 
| 141 | + | args_info->staticProps_group_counter = 0 ; | 
| 142 | + | } | 
| 143 | + |  | 
| 144 | + | static | 
| 145 | + | void clear_args (struct gengetopt_args_info *args_info) | 
| 146 | + | { | 
| 147 | + | args_info->input_arg = NULL; | 
| 148 | + | args_info->input_orig = NULL; | 
| 149 | + | args_info->output_arg = NULL; | 
| 150 | + | args_info->output_orig = NULL; | 
| 151 | + | args_info->step_arg = 1; | 
| 152 | + | args_info->step_orig = NULL; | 
| 153 | + | args_info->nbins_arg = 100; | 
| 154 | + | args_info->nbins_orig = NULL; | 
| 155 | + | args_info->nbins_x_arg = 100; | 
| 156 | + | args_info->nbins_x_orig = NULL; | 
| 157 | + | args_info->nbins_y_arg = 100; | 
| 158 | + | args_info->nbins_y_orig = NULL; | 
| 159 | + | args_info->nbins_z_arg = 100; | 
| 160 | + | args_info->nbins_z_orig = NULL; | 
| 161 | + | args_info->nanglebins_arg = 50; | 
| 162 | + | args_info->nanglebins_orig = NULL; | 
| 163 | + | args_info->length_orig = NULL; | 
| 164 | + | args_info->rcut_orig = NULL; | 
| 165 | + | args_info->zoffset_arg = 0; | 
| 166 | + | args_info->zoffset_orig = NULL; | 
| 167 | + | args_info->sele1_arg = NULL; | 
| 168 | + | args_info->sele1_orig = NULL; | 
| 169 | + | args_info->sele2_arg = NULL; | 
| 170 | + | args_info->sele2_orig = NULL; | 
| 171 | + | args_info->sele3_arg = NULL; | 
| 172 | + | args_info->sele3_orig = NULL; | 
| 173 | + | args_info->refsele_arg = NULL; | 
| 174 | + | args_info->refsele_orig = NULL; | 
| 175 | + | args_info->comsele_arg = NULL; | 
| 176 | + | args_info->comsele_orig = NULL; | 
| 177 | + | args_info->molname_arg = NULL; | 
| 178 | + | args_info->molname_orig = NULL; | 
| 179 | + | args_info->begin_orig = NULL; | 
| 180 | + | args_info->end_orig = NULL; | 
| 181 | + | args_info->radius_orig = NULL; | 
| 182 | + |  | 
| 183 | + | } | 
| 184 | + |  | 
| 185 | + | static | 
| 186 | + | void init_args_info(struct gengetopt_args_info *args_info) | 
| 187 | + | { | 
| 188 | + |  | 
| 189 | + |  | 
| 190 | + | args_info->help_help = gengetopt_args_info_help[0] ; | 
| 191 | + | args_info->version_help = gengetopt_args_info_help[1] ; | 
| 192 | + | args_info->input_help = gengetopt_args_info_help[2] ; | 
| 193 | + | args_info->output_help = gengetopt_args_info_help[3] ; | 
| 194 | + | args_info->step_help = gengetopt_args_info_help[4] ; | 
| 195 | + | args_info->nbins_help = gengetopt_args_info_help[5] ; | 
| 196 | + | args_info->nbins_x_help = gengetopt_args_info_help[6] ; | 
| 197 | + | args_info->nbins_y_help = gengetopt_args_info_help[7] ; | 
| 198 | + | args_info->nbins_z_help = gengetopt_args_info_help[8] ; | 
| 199 | + | args_info->nanglebins_help = gengetopt_args_info_help[9] ; | 
| 200 | + | args_info->length_help = gengetopt_args_info_help[10] ; | 
| 201 | + | args_info->rcut_help = gengetopt_args_info_help[11] ; | 
| 202 | + | args_info->zoffset_help = gengetopt_args_info_help[12] ; | 
| 203 | + | args_info->sele1_help = gengetopt_args_info_help[13] ; | 
| 204 | + | args_info->sele2_help = gengetopt_args_info_help[14] ; | 
| 205 | + | args_info->sele3_help = gengetopt_args_info_help[15] ; | 
| 206 | + | args_info->refsele_help = gengetopt_args_info_help[16] ; | 
| 207 | + | args_info->comsele_help = gengetopt_args_info_help[17] ; | 
| 208 | + | args_info->molname_help = gengetopt_args_info_help[18] ; | 
| 209 | + | args_info->begin_help = gengetopt_args_info_help[19] ; | 
| 210 | + | args_info->end_help = gengetopt_args_info_help[20] ; | 
| 211 | + | args_info->radius_help = gengetopt_args_info_help[21] ; | 
| 212 | + | args_info->bo_help = gengetopt_args_info_help[23] ; | 
| 213 | + | args_info->bor_help = gengetopt_args_info_help[24] ; | 
| 214 | + | args_info->bad_help = gengetopt_args_info_help[25] ; | 
| 215 | + | args_info->gofr_help = gengetopt_args_info_help[26] ; | 
| 216 | + | args_info->gofz_help = gengetopt_args_info_help[27] ; | 
| 217 | + | args_info->r_theta_help = gengetopt_args_info_help[28] ; | 
| 218 | + | args_info->r_omega_help = gengetopt_args_info_help[29] ; | 
| 219 | + | args_info->r_z_help = gengetopt_args_info_help[30] ; | 
| 220 | + | args_info->theta_omega_help = gengetopt_args_info_help[31] ; | 
| 221 | + | args_info->gxyz_help = gengetopt_args_info_help[32] ; | 
| 222 | + | args_info->p2_help = gengetopt_args_info_help[33] ; | 
| 223 | + | args_info->rp2_help = gengetopt_args_info_help[34] ; | 
| 224 | + | args_info->scd_help = gengetopt_args_info_help[35] ; | 
| 225 | + | args_info->density_help = gengetopt_args_info_help[36] ; | 
| 226 | + | args_info->slab_density_help = gengetopt_args_info_help[37] ; | 
| 227 | + | args_info->p_angle_help = gengetopt_args_info_help[38] ; | 
| 228 | + | args_info->hxy_help = gengetopt_args_info_help[39] ; | 
| 229 | + | args_info->rho_r_help = gengetopt_args_info_help[40] ; | 
| 230 | + | args_info->hullvol_help = gengetopt_args_info_help[41] ; | 
| 231 | + |  | 
| 232 | + | } | 
| 233 | + |  | 
| 234 |  | void | 
| 235 |  | cmdline_parser_print_version (void) | 
| 236 |  | { | 
| 237 |  | printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION); | 
| 238 |  | } | 
| 239 |  |  | 
| 240 | + | static void print_help_common(void) { | 
| 241 | + | cmdline_parser_print_version (); | 
| 242 | + |  | 
| 243 | + | if (strlen(gengetopt_args_info_purpose) > 0) | 
| 244 | + | printf("\n%s\n", gengetopt_args_info_purpose); | 
| 245 | + |  | 
| 246 | + | if (strlen(gengetopt_args_info_usage) > 0) | 
| 247 | + | printf("\n%s\n", gengetopt_args_info_usage); | 
| 248 | + |  | 
| 249 | + | printf("\n"); | 
| 250 | + |  | 
| 251 | + | if (strlen(gengetopt_args_info_description) > 0) | 
| 252 | + | printf("%s\n", gengetopt_args_info_description); | 
| 253 | + | } | 
| 254 | + |  | 
| 255 |  | void | 
| 256 |  | cmdline_parser_print_help (void) | 
| 257 |  | { | 
| 258 | < | cmdline_parser_print_version (); | 
| 259 | < | printf("\n" | 
| 260 | < | "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE); | 
| 261 | < | printf("\n"); | 
| 38 | < | printf("  -h, --help                      Print help and exit\n"); | 
| 39 | < | printf("  -V, --version                   Print version and exit\n"); | 
| 40 | < | printf("  -i, --input=filename            input dump file\n"); | 
| 41 | < | printf("  -o, --output=filename           output file name\n"); | 
| 42 | < | printf("  -n, --step=INT                  process every n frame  (default=`1')\n"); | 
| 43 | < | printf("  -r, --nrbins=INT                number of bins for distance  (default=`100')\n"); | 
| 44 | < | printf("  -a, --nanglebins=INT            number of bins for cos(angle)  (default=\n                                    `50')\n"); | 
| 45 | < | printf("  -l, --length=DOUBLE             maximum length (Defaults to 1/2 smallest \n                                    length of first frame)\n"); | 
| 46 | < | printf("      --sele1=selection script    select the first stuntdouble set\n"); | 
| 47 | < | printf("      --sele2=selection script    select the second stuntdouble set\n"); | 
| 48 | < | printf("      --sele3=selection script    select the third stuntdouble set\n"); | 
| 49 | < | printf("      --refsele=selection script  select reference (use and only use with \n                                    --gxyz)\n"); | 
| 50 | < | printf("      --molname=STRING            molecule name\n"); | 
| 51 | < | printf("      --begin=INT                 begin interanl index\n"); | 
| 52 | < | printf("      --end=INT                   end internal index\n"); | 
| 53 | < | printf("\n"); | 
| 54 | < | printf(" Group: staticProps  an option of this group is required\n"); | 
| 55 | < | printf("      --gofr                      g(r)\n"); | 
| 56 | < | printf("      --r_theta                   g(r, cos(theta))\n"); | 
| 57 | < | printf("      --r_omega                   g(r, cos(omega))\n"); | 
| 58 | < | printf("      --theta_omega               g(cos(theta), cos(omega))\n"); | 
| 59 | < | printf("      --gxyz                      g(x, y, z)\n"); | 
| 60 | < | printf("      --p2                        p2 order parameter (--sele1 and --sele2 must \n                                    be specified)\n"); | 
| 61 | < | printf("      --scd                       scd order parameter(either --sele1, --sele2, \n                                    --sele3 are specified or --molname, \n                                    --begin, --end are specified)\n"); | 
| 258 | > | int i = 0; | 
| 259 | > | print_help_common(); | 
| 260 | > | while (gengetopt_args_info_help[i]) | 
| 261 | > | printf("%s\n", gengetopt_args_info_help[i++]); | 
| 262 |  | } | 
| 263 |  |  | 
| 264 | + | void | 
| 265 | + | cmdline_parser_init (struct gengetopt_args_info *args_info) | 
| 266 | + | { | 
| 267 | + | clear_given (args_info); | 
| 268 | + | clear_args (args_info); | 
| 269 | + | init_args_info (args_info); | 
| 270 |  |  | 
| 271 | < | static char *gengetopt_strdup (const char *s); | 
| 271 | > | args_info->inputs = NULL; | 
| 272 | > | args_info->inputs_num = 0; | 
| 273 | > | } | 
| 274 |  |  | 
| 275 | < | /* gengetopt_strdup() */ | 
| 276 | < | /* strdup.c replacement of strdup, which is not standard */ | 
| 275 | > | void | 
| 276 | > | cmdline_parser_params_init(struct cmdline_parser_params *params) | 
| 277 | > | { | 
| 278 | > | if (params) | 
| 279 | > | { | 
| 280 | > | params->override = 0; | 
| 281 | > | params->initialize = 1; | 
| 282 | > | params->check_required = 1; | 
| 283 | > | params->check_ambiguity = 0; | 
| 284 | > | params->print_errors = 1; | 
| 285 | > | } | 
| 286 | > | } | 
| 287 | > |  | 
| 288 | > | struct cmdline_parser_params * | 
| 289 | > | cmdline_parser_params_create(void) | 
| 290 | > | { | 
| 291 | > | struct cmdline_parser_params *params = | 
| 292 | > | (struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params)); | 
| 293 | > | cmdline_parser_params_init(params); | 
| 294 | > | return params; | 
| 295 | > | } | 
| 296 | > |  | 
| 297 | > | static void | 
| 298 | > | free_string_field (char **s) | 
| 299 | > | { | 
| 300 | > | if (*s) | 
| 301 | > | { | 
| 302 | > | free (*s); | 
| 303 | > | *s = 0; | 
| 304 | > | } | 
| 305 | > | } | 
| 306 | > |  | 
| 307 | > |  | 
| 308 | > | static void | 
| 309 | > | cmdline_parser_release (struct gengetopt_args_info *args_info) | 
| 310 | > | { | 
| 311 | > | unsigned int i; | 
| 312 | > | free_string_field (&(args_info->input_arg)); | 
| 313 | > | free_string_field (&(args_info->input_orig)); | 
| 314 | > | free_string_field (&(args_info->output_arg)); | 
| 315 | > | free_string_field (&(args_info->output_orig)); | 
| 316 | > | free_string_field (&(args_info->step_orig)); | 
| 317 | > | free_string_field (&(args_info->nbins_orig)); | 
| 318 | > | free_string_field (&(args_info->nbins_x_orig)); | 
| 319 | > | free_string_field (&(args_info->nbins_y_orig)); | 
| 320 | > | free_string_field (&(args_info->nbins_z_orig)); | 
| 321 | > | free_string_field (&(args_info->nanglebins_orig)); | 
| 322 | > | free_string_field (&(args_info->length_orig)); | 
| 323 | > | free_string_field (&(args_info->rcut_orig)); | 
| 324 | > | free_string_field (&(args_info->zoffset_orig)); | 
| 325 | > | free_string_field (&(args_info->sele1_arg)); | 
| 326 | > | free_string_field (&(args_info->sele1_orig)); | 
| 327 | > | free_string_field (&(args_info->sele2_arg)); | 
| 328 | > | free_string_field (&(args_info->sele2_orig)); | 
| 329 | > | free_string_field (&(args_info->sele3_arg)); | 
| 330 | > | free_string_field (&(args_info->sele3_orig)); | 
| 331 | > | free_string_field (&(args_info->refsele_arg)); | 
| 332 | > | free_string_field (&(args_info->refsele_orig)); | 
| 333 | > | free_string_field (&(args_info->comsele_arg)); | 
| 334 | > | free_string_field (&(args_info->comsele_orig)); | 
| 335 | > | free_string_field (&(args_info->molname_arg)); | 
| 336 | > | free_string_field (&(args_info->molname_orig)); | 
| 337 | > | free_string_field (&(args_info->begin_orig)); | 
| 338 | > | free_string_field (&(args_info->end_orig)); | 
| 339 | > | free_string_field (&(args_info->radius_orig)); | 
| 340 | > |  | 
| 341 | > |  | 
| 342 | > | for (i = 0; i < args_info->inputs_num; ++i) | 
| 343 | > | free (args_info->inputs [i]); | 
| 344 | > |  | 
| 345 | > | if (args_info->inputs_num) | 
| 346 | > | free (args_info->inputs); | 
| 347 | > |  | 
| 348 | > | clear_given (args_info); | 
| 349 | > | } | 
| 350 | > |  | 
| 351 | > |  | 
| 352 | > | static void | 
| 353 | > | write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[]) | 
| 354 | > | { | 
| 355 | > | if (arg) { | 
| 356 | > | fprintf(outfile, "%s=\"%s\"\n", opt, arg); | 
| 357 | > | } else { | 
| 358 | > | fprintf(outfile, "%s\n", opt); | 
| 359 | > | } | 
| 360 | > | } | 
| 361 | > |  | 
| 362 | > |  | 
| 363 | > | int | 
| 364 | > | cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info) | 
| 365 | > | { | 
| 366 | > | int i = 0; | 
| 367 | > |  | 
| 368 | > | if (!outfile) | 
| 369 | > | { | 
| 370 | > | fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE); | 
| 371 | > | return EXIT_FAILURE; | 
| 372 | > | } | 
| 373 | > |  | 
| 374 | > | if (args_info->help_given) | 
| 375 | > | write_into_file(outfile, "help", 0, 0 ); | 
| 376 | > | if (args_info->version_given) | 
| 377 | > | write_into_file(outfile, "version", 0, 0 ); | 
| 378 | > | if (args_info->input_given) | 
| 379 | > | write_into_file(outfile, "input", args_info->input_orig, 0); | 
| 380 | > | if (args_info->output_given) | 
| 381 | > | write_into_file(outfile, "output", args_info->output_orig, 0); | 
| 382 | > | if (args_info->step_given) | 
| 383 | > | write_into_file(outfile, "step", args_info->step_orig, 0); | 
| 384 | > | if (args_info->nbins_given) | 
| 385 | > | write_into_file(outfile, "nbins", args_info->nbins_orig, 0); | 
| 386 | > | if (args_info->nbins_x_given) | 
| 387 | > | write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0); | 
| 388 | > | if (args_info->nbins_y_given) | 
| 389 | > | write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0); | 
| 390 | > | if (args_info->nbins_z_given) | 
| 391 | > | write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0); | 
| 392 | > | if (args_info->nanglebins_given) | 
| 393 | > | write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0); | 
| 394 | > | if (args_info->length_given) | 
| 395 | > | write_into_file(outfile, "length", args_info->length_orig, 0); | 
| 396 | > | if (args_info->rcut_given) | 
| 397 | > | write_into_file(outfile, "rcut", args_info->rcut_orig, 0); | 
| 398 | > | if (args_info->zoffset_given) | 
| 399 | > | write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0); | 
| 400 | > | if (args_info->sele1_given) | 
| 401 | > | write_into_file(outfile, "sele1", args_info->sele1_orig, 0); | 
| 402 | > | if (args_info->sele2_given) | 
| 403 | > | write_into_file(outfile, "sele2", args_info->sele2_orig, 0); | 
| 404 | > | if (args_info->sele3_given) | 
| 405 | > | write_into_file(outfile, "sele3", args_info->sele3_orig, 0); | 
| 406 | > | if (args_info->refsele_given) | 
| 407 | > | write_into_file(outfile, "refsele", args_info->refsele_orig, 0); | 
| 408 | > | if (args_info->comsele_given) | 
| 409 | > | write_into_file(outfile, "comsele", args_info->comsele_orig, 0); | 
| 410 | > | if (args_info->molname_given) | 
| 411 | > | write_into_file(outfile, "molname", args_info->molname_orig, 0); | 
| 412 | > | if (args_info->begin_given) | 
| 413 | > | write_into_file(outfile, "begin", args_info->begin_orig, 0); | 
| 414 | > | if (args_info->end_given) | 
| 415 | > | write_into_file(outfile, "end", args_info->end_orig, 0); | 
| 416 | > | if (args_info->radius_given) | 
| 417 | > | write_into_file(outfile, "radius", args_info->radius_orig, 0); | 
| 418 | > | if (args_info->bo_given) | 
| 419 | > | write_into_file(outfile, "bo", 0, 0 ); | 
| 420 | > | if (args_info->bor_given) | 
| 421 | > | write_into_file(outfile, "bor", 0, 0 ); | 
| 422 | > | if (args_info->bad_given) | 
| 423 | > | write_into_file(outfile, "bad", 0, 0 ); | 
| 424 | > | if (args_info->gofr_given) | 
| 425 | > | write_into_file(outfile, "gofr", 0, 0 ); | 
| 426 | > | if (args_info->gofz_given) | 
| 427 | > | write_into_file(outfile, "gofz", 0, 0 ); | 
| 428 | > | if (args_info->r_theta_given) | 
| 429 | > | write_into_file(outfile, "r_theta", 0, 0 ); | 
| 430 | > | if (args_info->r_omega_given) | 
| 431 | > | write_into_file(outfile, "r_omega", 0, 0 ); | 
| 432 | > | if (args_info->r_z_given) | 
| 433 | > | write_into_file(outfile, "r_z", 0, 0 ); | 
| 434 | > | if (args_info->theta_omega_given) | 
| 435 | > | write_into_file(outfile, "theta_omega", 0, 0 ); | 
| 436 | > | if (args_info->gxyz_given) | 
| 437 | > | write_into_file(outfile, "gxyz", 0, 0 ); | 
| 438 | > | if (args_info->p2_given) | 
| 439 | > | write_into_file(outfile, "p2", 0, 0 ); | 
| 440 | > | if (args_info->rp2_given) | 
| 441 | > | write_into_file(outfile, "rp2", 0, 0 ); | 
| 442 | > | if (args_info->scd_given) | 
| 443 | > | write_into_file(outfile, "scd", 0, 0 ); | 
| 444 | > | if (args_info->density_given) | 
| 445 | > | write_into_file(outfile, "density", 0, 0 ); | 
| 446 | > | if (args_info->slab_density_given) | 
| 447 | > | write_into_file(outfile, "slab_density", 0, 0 ); | 
| 448 | > | if (args_info->p_angle_given) | 
| 449 | > | write_into_file(outfile, "p_angle", 0, 0 ); | 
| 450 | > | if (args_info->hxy_given) | 
| 451 | > | write_into_file(outfile, "hxy", 0, 0 ); | 
| 452 | > | if (args_info->rho_r_given) | 
| 453 | > | write_into_file(outfile, "rho_r", 0, 0 ); | 
| 454 | > | if (args_info->hullvol_given) | 
| 455 | > | write_into_file(outfile, "hullvol", 0, 0 ); | 
| 456 | > |  | 
| 457 | > |  | 
| 458 | > | i = EXIT_SUCCESS; | 
| 459 | > | return i; | 
| 460 | > | } | 
| 461 | > |  | 
| 462 | > | int | 
| 463 | > | cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info) | 
| 464 | > | { | 
| 465 | > | FILE *outfile; | 
| 466 | > | int i = 0; | 
| 467 | > |  | 
| 468 | > | outfile = fopen(filename, "w"); | 
| 469 | > |  | 
| 470 | > | if (!outfile) | 
| 471 | > | { | 
| 472 | > | fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename); | 
| 473 | > | return EXIT_FAILURE; | 
| 474 | > | } | 
| 475 | > |  | 
| 476 | > | i = cmdline_parser_dump(outfile, args_info); | 
| 477 | > | fclose (outfile); | 
| 478 | > |  | 
| 479 | > | return i; | 
| 480 | > | } | 
| 481 | > |  | 
| 482 | > | void | 
| 483 | > | cmdline_parser_free (struct gengetopt_args_info *args_info) | 
| 484 | > | { | 
| 485 | > | cmdline_parser_release (args_info); | 
| 486 | > | } | 
| 487 | > |  | 
| 488 | > | /** @brief replacement of strdup, which is not standard */ | 
| 489 |  | char * | 
| 490 |  | gengetopt_strdup (const char *s) | 
| 491 |  | { | 
| 492 | < | char *result = (char*)malloc(strlen(s) + 1); | 
| 492 | > | char *result = NULL; | 
| 493 | > | if (!s) | 
| 494 | > | return result; | 
| 495 | > |  | 
| 496 | > | result = (char*)malloc(strlen(s) + 1); | 
| 497 |  | if (result == (char*)0) | 
| 498 |  | return (char*)0; | 
| 499 |  | strcpy(result, s); | 
| 500 |  | return result; | 
| 501 |  | } | 
| 502 |  |  | 
| 503 | < | int | 
| 504 | < | cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) | 
| 503 | > | static void | 
| 504 | > | reset_group_staticProps(struct gengetopt_args_info *args_info) | 
| 505 |  | { | 
| 506 | < | int c;        /* Character of the parsed option.  */ | 
| 507 | < | int missing_required_options = 0; | 
| 84 | < | int staticProps_group_counter = 0; | 
| 506 | > | if (! args_info->staticProps_group_counter) | 
| 507 | > | return; | 
| 508 |  |  | 
| 509 | < |  | 
| 510 | < | args_info->help_given = 0 ; | 
| 511 | < | args_info->version_given = 0 ; | 
| 89 | < | args_info->input_given = 0 ; | 
| 90 | < | args_info->output_given = 0 ; | 
| 91 | < | args_info->step_given = 0 ; | 
| 92 | < | args_info->nrbins_given = 0 ; | 
| 93 | < | args_info->nanglebins_given = 0 ; | 
| 94 | < | args_info->length_given = 0 ; | 
| 95 | < | args_info->sele1_given = 0 ; | 
| 96 | < | args_info->sele2_given = 0 ; | 
| 97 | < | args_info->sele3_given = 0 ; | 
| 98 | < | args_info->refsele_given = 0 ; | 
| 99 | < | args_info->molname_given = 0 ; | 
| 100 | < | args_info->begin_given = 0 ; | 
| 101 | < | args_info->end_given = 0 ; | 
| 509 | > | args_info->bo_given = 0 ; | 
| 510 | > | args_info->bor_given = 0 ; | 
| 511 | > | args_info->bad_given = 0 ; | 
| 512 |  | args_info->gofr_given = 0 ; | 
| 513 | + | args_info->gofz_given = 0 ; | 
| 514 |  | args_info->r_theta_given = 0 ; | 
| 515 |  | args_info->r_omega_given = 0 ; | 
| 516 | + | args_info->r_z_given = 0 ; | 
| 517 |  | args_info->theta_omega_given = 0 ; | 
| 518 |  | args_info->gxyz_given = 0 ; | 
| 519 |  | args_info->p2_given = 0 ; | 
| 520 | + | args_info->rp2_given = 0 ; | 
| 521 |  | args_info->scd_given = 0 ; | 
| 522 | < | #define clear_args() { \ | 
| 523 | < | args_info->input_arg = NULL; \ | 
| 524 | < | args_info->output_arg = NULL; \ | 
| 525 | < | args_info->step_arg = 1 ;\ | 
| 526 | < | args_info->nrbins_arg = 100 ;\ | 
| 527 | < | args_info->nanglebins_arg = 50 ;\ | 
| 528 | < | args_info->sele1_arg = NULL; \ | 
| 529 | < | args_info->sele2_arg = NULL; \ | 
| 117 | < | args_info->sele3_arg = NULL; \ | 
| 118 | < | args_info->refsele_arg = NULL; \ | 
| 119 | < | args_info->molname_arg = NULL; \ | 
| 522 | > | args_info->density_given = 0 ; | 
| 523 | > | args_info->slab_density_given = 0 ; | 
| 524 | > | args_info->p_angle_given = 0 ; | 
| 525 | > | args_info->hxy_given = 0 ; | 
| 526 | > | args_info->rho_r_given = 0 ; | 
| 527 | > | args_info->hullvol_given = 0 ; | 
| 528 | > |  | 
| 529 | > | args_info->staticProps_group_counter = 0; | 
| 530 |  | } | 
| 531 |  |  | 
| 532 | < | clear_args(); | 
| 532 | > | int | 
| 533 | > | cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info) | 
| 534 | > | { | 
| 535 | > | return cmdline_parser2 (argc, argv, args_info, 0, 1, 1); | 
| 536 | > | } | 
| 537 |  |  | 
| 538 | + | int | 
| 539 | + | cmdline_parser_ext (int argc, char * const *argv, struct gengetopt_args_info *args_info, | 
| 540 | + | struct cmdline_parser_params *params) | 
| 541 | + | { | 
| 542 | + | int result; | 
| 543 | + | result = cmdline_parser_internal (argc, argv, args_info, params, NULL); | 
| 544 | + |  | 
| 545 | + | if (result == EXIT_FAILURE) | 
| 546 | + | { | 
| 547 | + | cmdline_parser_free (args_info); | 
| 548 | + | exit (EXIT_FAILURE); | 
| 549 | + | } | 
| 550 | + |  | 
| 551 | + | return result; | 
| 552 | + | } | 
| 553 | + |  | 
| 554 | + | int | 
| 555 | + | cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required) | 
| 556 | + | { | 
| 557 | + | int result; | 
| 558 | + | struct cmdline_parser_params params; | 
| 559 | + |  | 
| 560 | + | params.override = override; | 
| 561 | + | params.initialize = initialize; | 
| 562 | + | params.check_required = check_required; | 
| 563 | + | params.check_ambiguity = 0; | 
| 564 | + | params.print_errors = 1; | 
| 565 | + |  | 
| 566 | + | result = cmdline_parser_internal (argc, argv, args_info, ¶ms, NULL); | 
| 567 | + |  | 
| 568 | + | if (result == EXIT_FAILURE) | 
| 569 | + | { | 
| 570 | + | cmdline_parser_free (args_info); | 
| 571 | + | exit (EXIT_FAILURE); | 
| 572 | + | } | 
| 573 | + |  | 
| 574 | + | return result; | 
| 575 | + | } | 
| 576 | + |  | 
| 577 | + | int | 
| 578 | + | cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name) | 
| 579 | + | { | 
| 580 | + | int result = EXIT_SUCCESS; | 
| 581 | + |  | 
| 582 | + | if (cmdline_parser_required2(args_info, prog_name, NULL) > 0) | 
| 583 | + | result = EXIT_FAILURE; | 
| 584 | + |  | 
| 585 | + | if (result == EXIT_FAILURE) | 
| 586 | + | { | 
| 587 | + | cmdline_parser_free (args_info); | 
| 588 | + | exit (EXIT_FAILURE); | 
| 589 | + | } | 
| 590 | + |  | 
| 591 | + | return result; | 
| 592 | + | } | 
| 593 | + |  | 
| 594 | + | int | 
| 595 | + | cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error) | 
| 596 | + | { | 
| 597 | + | int error = 0; | 
| 598 | + |  | 
| 599 | + | /* checks for required options */ | 
| 600 | + | if (! args_info->input_given) | 
| 601 | + | { | 
| 602 | + | fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : "")); | 
| 603 | + | error = 1; | 
| 604 | + | } | 
| 605 | + |  | 
| 606 | + | if (args_info->staticProps_group_counter == 0) | 
| 607 | + | { | 
| 608 | + | fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : "")); | 
| 609 | + | error = 1; | 
| 610 | + | } | 
| 611 | + |  | 
| 612 | + |  | 
| 613 | + | /* checks for dependences among options */ | 
| 614 | + |  | 
| 615 | + | return error; | 
| 616 | + | } | 
| 617 | + |  | 
| 618 | + |  | 
| 619 | + | static char *package_name = 0; | 
| 620 | + |  | 
| 621 | + | /** | 
| 622 | + | * @brief updates an option | 
| 623 | + | * @param field the generic pointer to the field to update | 
| 624 | + | * @param orig_field the pointer to the orig field | 
| 625 | + | * @param field_given the pointer to the number of occurrence of this option | 
| 626 | + | * @param prev_given the pointer to the number of occurrence already seen | 
| 627 | + | * @param value the argument for this option (if null no arg was specified) | 
| 628 | + | * @param possible_values the possible values for this option (if specified) | 
| 629 | + | * @param default_value the default value (in case the option only accepts fixed values) | 
| 630 | + | * @param arg_type the type of this option | 
| 631 | + | * @param check_ambiguity @see cmdline_parser_params.check_ambiguity | 
| 632 | + | * @param override @see cmdline_parser_params.override | 
| 633 | + | * @param no_free whether to free a possible previous value | 
| 634 | + | * @param multiple_option whether this is a multiple option | 
| 635 | + | * @param long_opt the corresponding long option | 
| 636 | + | * @param short_opt the corresponding short option (or '-' if none) | 
| 637 | + | * @param additional_error possible further error specification | 
| 638 | + | */ | 
| 639 | + | static | 
| 640 | + | int update_arg(void *field, char **orig_field, | 
| 641 | + | unsigned int *field_given, unsigned int *prev_given, | 
| 642 | + | char *value, char *possible_values[], const char *default_value, | 
| 643 | + | cmdline_parser_arg_type arg_type, | 
| 644 | + | int check_ambiguity, int override, | 
| 645 | + | int no_free, int multiple_option, | 
| 646 | + | const char *long_opt, char short_opt, | 
| 647 | + | const char *additional_error) | 
| 648 | + | { | 
| 649 | + | char *stop_char = 0; | 
| 650 | + | const char *val = value; | 
| 651 | + | int found; | 
| 652 | + | char **string_field; | 
| 653 | + |  | 
| 654 | + | stop_char = 0; | 
| 655 | + | found = 0; | 
| 656 | + |  | 
| 657 | + | if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given))) | 
| 658 | + | { | 
| 659 | + | if (short_opt != '-') | 
| 660 | + | fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", | 
| 661 | + | package_name, long_opt, short_opt, | 
| 662 | + | (additional_error ? additional_error : "")); | 
| 663 | + | else | 
| 664 | + | fprintf (stderr, "%s: `--%s' option given more than once%s\n", | 
| 665 | + | package_name, long_opt, | 
| 666 | + | (additional_error ? additional_error : "")); | 
| 667 | + | return 1; /* failure */ | 
| 668 | + | } | 
| 669 | + |  | 
| 670 | + |  | 
| 671 | + | if (field_given && *field_given && ! override) | 
| 672 | + | return 0; | 
| 673 | + | if (prev_given) | 
| 674 | + | (*prev_given)++; | 
| 675 | + | if (field_given) | 
| 676 | + | (*field_given)++; | 
| 677 | + | if (possible_values) | 
| 678 | + | val = possible_values[found]; | 
| 679 | + |  | 
| 680 | + | switch(arg_type) { | 
| 681 | + | case ARG_INT: | 
| 682 | + | if (val) *((int *)field) = strtol (val, &stop_char, 0); | 
| 683 | + | break; | 
| 684 | + | case ARG_DOUBLE: | 
| 685 | + | if (val) *((double *)field) = strtod (val, &stop_char); | 
| 686 | + | break; | 
| 687 | + | case ARG_STRING: | 
| 688 | + | if (val) { | 
| 689 | + | string_field = (char **)field; | 
| 690 | + | if (!no_free && *string_field) | 
| 691 | + | free (*string_field); /* free previous string */ | 
| 692 | + | *string_field = gengetopt_strdup (val); | 
| 693 | + | } | 
| 694 | + | break; | 
| 695 | + | default: | 
| 696 | + | break; | 
| 697 | + | }; | 
| 698 | + |  | 
| 699 | + | /* check numeric conversion */ | 
| 700 | + | switch(arg_type) { | 
| 701 | + | case ARG_INT: | 
| 702 | + | case ARG_DOUBLE: | 
| 703 | + | if (val && !(stop_char && *stop_char == '\0')) { | 
| 704 | + | fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val); | 
| 705 | + | return 1; /* failure */ | 
| 706 | + | } | 
| 707 | + | break; | 
| 708 | + | default: | 
| 709 | + | ; | 
| 710 | + | }; | 
| 711 | + |  | 
| 712 | + | /* store the original value */ | 
| 713 | + | switch(arg_type) { | 
| 714 | + | case ARG_NO: | 
| 715 | + | break; | 
| 716 | + | default: | 
| 717 | + | if (value && orig_field) { | 
| 718 | + | if (no_free) { | 
| 719 | + | *orig_field = value; | 
| 720 | + | } else { | 
| 721 | + | if (*orig_field) | 
| 722 | + | free (*orig_field); /* free previous string */ | 
| 723 | + | *orig_field = gengetopt_strdup (value); | 
| 724 | + | } | 
| 725 | + | } | 
| 726 | + | }; | 
| 727 | + |  | 
| 728 | + | return 0; /* OK */ | 
| 729 | + | } | 
| 730 | + |  | 
| 731 | + |  | 
| 732 | + | int | 
| 733 | + | cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, | 
| 734 | + | struct cmdline_parser_params *params, const char *additional_error) | 
| 735 | + | { | 
| 736 | + | int c;        /* Character of the parsed option.  */ | 
| 737 | + |  | 
| 738 | + | int error = 0; | 
| 739 | + | struct gengetopt_args_info local_args_info; | 
| 740 | + |  | 
| 741 | + | int override; | 
| 742 | + | int initialize; | 
| 743 | + | int check_required; | 
| 744 | + | int check_ambiguity; | 
| 745 | + |  | 
| 746 | + | package_name = argv[0]; | 
| 747 | + |  | 
| 748 | + | override = params->override; | 
| 749 | + | initialize = params->initialize; | 
| 750 | + | check_required = params->check_required; | 
| 751 | + | check_ambiguity = params->check_ambiguity; | 
| 752 | + |  | 
| 753 | + | if (initialize) | 
| 754 | + | cmdline_parser_init (args_info); | 
| 755 | + |  | 
| 756 | + | cmdline_parser_init (&local_args_info); | 
| 757 | + |  | 
| 758 |  | optarg = 0; | 
| 759 | < | optind = 1; | 
| 760 | < | opterr = 1; | 
| 759 | > | optind = 0; | 
| 760 | > | opterr = params->print_errors; | 
| 761 |  | optopt = '?'; | 
| 762 |  |  | 
| 763 |  | while (1) | 
| 764 |  | { | 
| 765 |  | int option_index = 0; | 
| 132 | – | char *stop_char; | 
| 766 |  |  | 
| 767 |  | static struct option long_options[] = { | 
| 768 |  | { "help",       0, NULL, 'h' }, | 
| 770 |  | { "input",      1, NULL, 'i' }, | 
| 771 |  | { "output",     1, NULL, 'o' }, | 
| 772 |  | { "step",       1, NULL, 'n' }, | 
| 773 | < | { "nrbins",     1, NULL, 'r' }, | 
| 773 | > | { "nbins",      1, NULL, 'b' }, | 
| 774 | > | { "nbins_x",    1, NULL, 'x' }, | 
| 775 | > | { "nbins_y",    1, NULL, 'y' }, | 
| 776 | > | { "nbins_z",    1, NULL, 0 }, | 
| 777 |  | { "nanglebins", 1, NULL, 'a' }, | 
| 778 | < | { "length",     1, NULL, 'l' }, | 
| 778 | > | { "length",     1, NULL, 0 }, | 
| 779 | > | { "rcut",       1, NULL, 'c' }, | 
| 780 | > | { "zoffset",    1, NULL, 'z' }, | 
| 781 |  | { "sele1",      1, NULL, 0 }, | 
| 782 |  | { "sele2",      1, NULL, 0 }, | 
| 783 |  | { "sele3",      1, NULL, 0 }, | 
| 784 |  | { "refsele",    1, NULL, 0 }, | 
| 785 | + | { "comsele",    1, NULL, 0 }, | 
| 786 |  | { "molname",    1, NULL, 0 }, | 
| 787 |  | { "begin",      1, NULL, 0 }, | 
| 788 |  | { "end",        1, NULL, 0 }, | 
| 789 | < | { "gofr",       0, NULL, 0 }, | 
| 789 | > | { "radius",     1, NULL, 0 }, | 
| 790 | > | { "bo", 0, NULL, 0 }, | 
| 791 | > | { "bor",        0, NULL, 0 }, | 
| 792 | > | { "bad",        0, NULL, 0 }, | 
| 793 | > | { "gofr",       0, NULL, 'g' }, | 
| 794 | > | { "gofz",       0, NULL, 0 }, | 
| 795 |  | { "r_theta",    0, NULL, 0 }, | 
| 796 |  | { "r_omega",    0, NULL, 0 }, | 
| 797 | + | { "r_z",        0, NULL, 0 }, | 
| 798 |  | { "theta_omega",        0, NULL, 0 }, | 
| 799 |  | { "gxyz",       0, NULL, 0 }, | 
| 800 | < | { "p2", 0, NULL, 0 }, | 
| 801 | < | { "scd",        0, NULL, 0 }, | 
| 800 | > | { "p2", 0, NULL, 'p' }, | 
| 801 | > | { "rp2",        0, NULL, 0 }, | 
| 802 | > | { "scd",        0, NULL, 's' }, | 
| 803 | > | { "density",    0, NULL, 'd' }, | 
| 804 | > | { "slab_density",       0, NULL, 0 }, | 
| 805 | > | { "p_angle",    0, NULL, 0 }, | 
| 806 | > | { "hxy",        0, NULL, 0 }, | 
| 807 | > | { "rho_r",      0, NULL, 0 }, | 
| 808 | > | { "hullvol",    0, NULL, 0 }, | 
| 809 |  | { NULL, 0, NULL, 0 } | 
| 810 |  | }; | 
| 811 |  |  | 
| 812 | < | stop_char = 0; | 
| 161 | < | c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index); | 
| 812 | > | c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsd", long_options, &option_index); | 
| 813 |  |  | 
| 814 |  | if (c == -1) break;       /* Exit from `while (1)' loop.  */ | 
| 815 |  |  | 
| 816 |  | switch (c) | 
| 817 |  | { | 
| 818 |  | case 'h':       /* Print help and exit.  */ | 
| 168 | – | clear_args (); | 
| 819 |  | cmdline_parser_print_help (); | 
| 820 | + | cmdline_parser_free (&local_args_info); | 
| 821 |  | exit (EXIT_SUCCESS); | 
| 822 |  |  | 
| 823 |  | case 'V':       /* Print version and exit.  */ | 
| 173 | – | clear_args (); | 
| 824 |  | cmdline_parser_print_version (); | 
| 825 | + | cmdline_parser_free (&local_args_info); | 
| 826 |  | exit (EXIT_SUCCESS); | 
| 827 |  |  | 
| 828 |  | case 'i':       /* input dump file.  */ | 
| 829 | < | if (args_info->input_given) | 
| 830 | < | { | 
| 831 | < | fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 832 | < | clear_args (); | 
| 833 | < | exit (EXIT_FAILURE); | 
| 834 | < | } | 
| 835 | < | args_info->input_given = 1; | 
| 836 | < | args_info->input_arg = gengetopt_strdup (optarg); | 
| 829 | > |  | 
| 830 | > |  | 
| 831 | > | if (update_arg( (void *)&(args_info->input_arg), | 
| 832 | > | &(args_info->input_orig), &(args_info->input_given), | 
| 833 | > | &(local_args_info.input_given), optarg, 0, 0, ARG_STRING, | 
| 834 | > | check_ambiguity, override, 0, 0, | 
| 835 | > | "input", 'i', | 
| 836 | > | additional_error)) | 
| 837 | > | goto failure; | 
| 838 | > |  | 
| 839 |  | break; | 
| 187 | – |  | 
| 840 |  | case 'o':       /* output file name.  */ | 
| 841 | < | if (args_info->output_given) | 
| 842 | < | { | 
| 843 | < | fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 844 | < | clear_args (); | 
| 845 | < | exit (EXIT_FAILURE); | 
| 846 | < | } | 
| 847 | < | args_info->output_given = 1; | 
| 848 | < | args_info->output_arg = gengetopt_strdup (optarg); | 
| 841 | > |  | 
| 842 | > |  | 
| 843 | > | if (update_arg( (void *)&(args_info->output_arg), | 
| 844 | > | &(args_info->output_orig), &(args_info->output_given), | 
| 845 | > | &(local_args_info.output_given), optarg, 0, 0, ARG_STRING, | 
| 846 | > | check_ambiguity, override, 0, 0, | 
| 847 | > | "output", 'o', | 
| 848 | > | additional_error)) | 
| 849 | > | goto failure; | 
| 850 | > |  | 
| 851 |  | break; | 
| 198 | – |  | 
| 852 |  | case 'n':       /* process every n frame.  */ | 
| 853 | < | if (args_info->step_given) | 
| 854 | < | { | 
| 855 | < | fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 856 | < | clear_args (); | 
| 857 | < | exit (EXIT_FAILURE); | 
| 858 | < | } | 
| 859 | < | args_info->step_given = 1; | 
| 860 | < | args_info->step_arg = strtol (optarg,&stop_char,0); | 
| 853 | > |  | 
| 854 | > |  | 
| 855 | > | if (update_arg( (void *)&(args_info->step_arg), | 
| 856 | > | &(args_info->step_orig), &(args_info->step_given), | 
| 857 | > | &(local_args_info.step_given), optarg, 0, "1", ARG_INT, | 
| 858 | > | check_ambiguity, override, 0, 0, | 
| 859 | > | "step", 'n', | 
| 860 | > | additional_error)) | 
| 861 | > | goto failure; | 
| 862 | > |  | 
| 863 |  | break; | 
| 864 | < |  | 
| 865 | < | case 'r':       /* number of bins for distance.  */ | 
| 866 | < | if (args_info->nrbins_given) | 
| 867 | < | { | 
| 868 | < | fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 869 | < | clear_args (); | 
| 870 | < | exit (EXIT_FAILURE); | 
| 871 | < | } | 
| 872 | < | args_info->nrbins_given = 1; | 
| 873 | < | args_info->nrbins_arg = strtol (optarg,&stop_char,0); | 
| 864 | > | case 'b':       /* number of bins (general purpose).  */ | 
| 865 | > |  | 
| 866 | > |  | 
| 867 | > | if (update_arg( (void *)&(args_info->nbins_arg), | 
| 868 | > | &(args_info->nbins_orig), &(args_info->nbins_given), | 
| 869 | > | &(local_args_info.nbins_given), optarg, 0, "100", ARG_INT, | 
| 870 | > | check_ambiguity, override, 0, 0, | 
| 871 | > | "nbins", 'b', | 
| 872 | > | additional_error)) | 
| 873 | > | goto failure; | 
| 874 | > |  | 
| 875 |  | break; | 
| 876 | < |  | 
| 876 | > | case 'x':       /* number of bins in x axis.  */ | 
| 877 | > |  | 
| 878 | > |  | 
| 879 | > | if (update_arg( (void *)&(args_info->nbins_x_arg), | 
| 880 | > | &(args_info->nbins_x_orig), &(args_info->nbins_x_given), | 
| 881 | > | &(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT, | 
| 882 | > | check_ambiguity, override, 0, 0, | 
| 883 | > | "nbins_x", 'x', | 
| 884 | > | additional_error)) | 
| 885 | > | goto failure; | 
| 886 | > |  | 
| 887 | > | break; | 
| 888 | > | case 'y':       /* number of bins in y axis.  */ | 
| 889 | > |  | 
| 890 | > |  | 
| 891 | > | if (update_arg( (void *)&(args_info->nbins_y_arg), | 
| 892 | > | &(args_info->nbins_y_orig), &(args_info->nbins_y_given), | 
| 893 | > | &(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT, | 
| 894 | > | check_ambiguity, override, 0, 0, | 
| 895 | > | "nbins_y", 'y', | 
| 896 | > | additional_error)) | 
| 897 | > | goto failure; | 
| 898 | > |  | 
| 899 | > | break; | 
| 900 |  | case 'a':       /* number of bins for cos(angle).  */ | 
| 901 | < | if (args_info->nanglebins_given) | 
| 902 | < | { | 
| 903 | < | fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 904 | < | clear_args (); | 
| 905 | < | exit (EXIT_FAILURE); | 
| 906 | < | } | 
| 907 | < | args_info->nanglebins_given = 1; | 
| 908 | < | args_info->nanglebins_arg = strtol (optarg,&stop_char,0); | 
| 901 | > |  | 
| 902 | > |  | 
| 903 | > | if (update_arg( (void *)&(args_info->nanglebins_arg), | 
| 904 | > | &(args_info->nanglebins_orig), &(args_info->nanglebins_given), | 
| 905 | > | &(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT, | 
| 906 | > | check_ambiguity, override, 0, 0, | 
| 907 | > | "nanglebins", 'a', | 
| 908 | > | additional_error)) | 
| 909 | > | goto failure; | 
| 910 | > |  | 
| 911 |  | break; | 
| 912 | < |  | 
| 913 | < | case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */ | 
| 914 | < | if (args_info->length_given) | 
| 915 | < | { | 
| 916 | < | fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 917 | < | clear_args (); | 
| 918 | < | exit (EXIT_FAILURE); | 
| 919 | < | } | 
| 920 | < | args_info->length_given = 1; | 
| 921 | < | args_info->length_arg = strtod (optarg, NULL); | 
| 912 | > | case 'c':       /* cutoff radius (rcut).  */ | 
| 913 | > |  | 
| 914 | > |  | 
| 915 | > | if (update_arg( (void *)&(args_info->rcut_arg), | 
| 916 | > | &(args_info->rcut_orig), &(args_info->rcut_given), | 
| 917 | > | &(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE, | 
| 918 | > | check_ambiguity, override, 0, 0, | 
| 919 | > | "rcut", 'c', | 
| 920 | > | additional_error)) | 
| 921 | > | goto failure; | 
| 922 | > |  | 
| 923 |  | break; | 
| 924 | + | case 'z':       /* Where to set the zero for the slab_density calculation.  */ | 
| 925 | + |  | 
| 926 | + |  | 
| 927 | + | if (update_arg( (void *)&(args_info->zoffset_arg), | 
| 928 | + | &(args_info->zoffset_orig), &(args_info->zoffset_given), | 
| 929 | + | &(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE, | 
| 930 | + | check_ambiguity, override, 0, 0, | 
| 931 | + | "zoffset", 'z', | 
| 932 | + | additional_error)) | 
| 933 | + | goto failure; | 
| 934 | + |  | 
| 935 | + | break; | 
| 936 | + | case 'g':       /* g(r).  */ | 
| 937 | + |  | 
| 938 | + | if (args_info->staticProps_group_counter && override) | 
| 939 | + | reset_group_staticProps (args_info); | 
| 940 | + | args_info->staticProps_group_counter += 1; | 
| 941 | + |  | 
| 942 | + | if (update_arg( 0 , | 
| 943 | + | 0 , &(args_info->gofr_given), | 
| 944 | + | &(local_args_info.gofr_given), optarg, 0, 0, ARG_NO, | 
| 945 | + | check_ambiguity, override, 0, 0, | 
| 946 | + | "gofr", 'g', | 
| 947 | + | additional_error)) | 
| 948 | + | goto failure; | 
| 949 | + |  | 
| 950 | + | break; | 
| 951 | + | case 'p':       /* p2 order parameter (--sele1 and --sele2 must be specified).  */ | 
| 952 | + |  | 
| 953 | + | if (args_info->staticProps_group_counter && override) | 
| 954 | + | reset_group_staticProps (args_info); | 
| 955 | + | args_info->staticProps_group_counter += 1; | 
| 956 | + |  | 
| 957 | + | if (update_arg( 0 , | 
| 958 | + | 0 , &(args_info->p2_given), | 
| 959 | + | &(local_args_info.p2_given), optarg, 0, 0, ARG_NO, | 
| 960 | + | check_ambiguity, override, 0, 0, | 
| 961 | + | "p2", 'p', | 
| 962 | + | additional_error)) | 
| 963 | + | goto failure; | 
| 964 | + |  | 
| 965 | + | break; | 
| 966 | + | case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */ | 
| 967 | + |  | 
| 968 | + | if (args_info->staticProps_group_counter && override) | 
| 969 | + | reset_group_staticProps (args_info); | 
| 970 | + | args_info->staticProps_group_counter += 1; | 
| 971 | + |  | 
| 972 | + | if (update_arg( 0 , | 
| 973 | + | 0 , &(args_info->scd_given), | 
| 974 | + | &(local_args_info.scd_given), optarg, 0, 0, ARG_NO, | 
| 975 | + | check_ambiguity, override, 0, 0, | 
| 976 | + | "scd", 's', | 
| 977 | + | additional_error)) | 
| 978 | + | goto failure; | 
| 979 | + |  | 
| 980 | + | break; | 
| 981 | + | case 'd':       /* density plot.  */ | 
| 982 | + |  | 
| 983 | + | if (args_info->staticProps_group_counter && override) | 
| 984 | + | reset_group_staticProps (args_info); | 
| 985 | + | args_info->staticProps_group_counter += 1; | 
| 986 | + |  | 
| 987 | + | if (update_arg( 0 , | 
| 988 | + | 0 , &(args_info->density_given), | 
| 989 | + | &(local_args_info.density_given), optarg, 0, 0, ARG_NO, | 
| 990 | + | check_ambiguity, override, 0, 0, | 
| 991 | + | "density", 'd', | 
| 992 | + | additional_error)) | 
| 993 | + | goto failure; | 
| 994 | + |  | 
| 995 | + | break; | 
| 996 |  |  | 
| 243 | – |  | 
| 997 |  | case 0: /* Long option with no short option */ | 
| 998 | < | /* select the first stuntdouble set.  */ | 
| 999 | < | if (strcmp (long_options[option_index].name, "sele1") == 0) | 
| 998 | > | /* number of bins in z axis.  */ | 
| 999 | > | if (strcmp (long_options[option_index].name, "nbins_z") == 0) | 
| 1000 |  | { | 
| 1001 | < | if (args_info->sele1_given) | 
| 1002 | < | { | 
| 1003 | < | fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 1004 | < | clear_args (); | 
| 1005 | < | exit (EXIT_FAILURE); | 
| 1006 | < | } | 
| 1007 | < | args_info->sele1_given = 1; | 
| 1008 | < | args_info->sele1_arg = gengetopt_strdup (optarg); | 
| 1009 | < | break; | 
| 1001 | > |  | 
| 1002 | > |  | 
| 1003 | > | if (update_arg( (void *)&(args_info->nbins_z_arg), | 
| 1004 | > | &(args_info->nbins_z_orig), &(args_info->nbins_z_given), | 
| 1005 | > | &(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT, | 
| 1006 | > | check_ambiguity, override, 0, 0, | 
| 1007 | > | "nbins_z", '-', | 
| 1008 | > | additional_error)) | 
| 1009 | > | goto failure; | 
| 1010 | > |  | 
| 1011 |  | } | 
| 1012 | + | /* maximum length (Defaults to 1/2 smallest length of first frame).  */ | 
| 1013 | + | else if (strcmp (long_options[option_index].name, "length") == 0) | 
| 1014 | + | { | 
| 1015 |  |  | 
| 1016 | + |  | 
| 1017 | + | if (update_arg( (void *)&(args_info->length_arg), | 
| 1018 | + | &(args_info->length_orig), &(args_info->length_given), | 
| 1019 | + | &(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE, | 
| 1020 | + | check_ambiguity, override, 0, 0, | 
| 1021 | + | "length", '-', | 
| 1022 | + | additional_error)) | 
| 1023 | + | goto failure; | 
| 1024 | + |  | 
| 1025 | + | } | 
| 1026 | + | /* select the first stuntdouble set.  */ | 
| 1027 | + | else if (strcmp (long_options[option_index].name, "sele1") == 0) | 
| 1028 | + | { | 
| 1029 | + |  | 
| 1030 | + |  | 
| 1031 | + | if (update_arg( (void *)&(args_info->sele1_arg), | 
| 1032 | + | &(args_info->sele1_orig), &(args_info->sele1_given), | 
| 1033 | + | &(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING, | 
| 1034 | + | check_ambiguity, override, 0, 0, | 
| 1035 | + | "sele1", '-', | 
| 1036 | + | additional_error)) | 
| 1037 | + | goto failure; | 
| 1038 | + |  | 
| 1039 | + | } | 
| 1040 |  | /* select the second stuntdouble set.  */ | 
| 1041 |  | else if (strcmp (long_options[option_index].name, "sele2") == 0) | 
| 1042 |  | { | 
| 262 | – | if (args_info->sele2_given) | 
| 263 | – | { | 
| 264 | – | fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 265 | – | clear_args (); | 
| 266 | – | exit (EXIT_FAILURE); | 
| 267 | – | } | 
| 268 | – | args_info->sele2_given = 1; | 
| 269 | – | args_info->sele2_arg = gengetopt_strdup (optarg); | 
| 270 | – | break; | 
| 271 | – | } | 
| 1043 |  |  | 
| 1044 | + |  | 
| 1045 | + | if (update_arg( (void *)&(args_info->sele2_arg), | 
| 1046 | + | &(args_info->sele2_orig), &(args_info->sele2_given), | 
| 1047 | + | &(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING, | 
| 1048 | + | check_ambiguity, override, 0, 0, | 
| 1049 | + | "sele2", '-', | 
| 1050 | + | additional_error)) | 
| 1051 | + | goto failure; | 
| 1052 | + |  | 
| 1053 | + | } | 
| 1054 |  | /* select the third stuntdouble set.  */ | 
| 1055 |  | else if (strcmp (long_options[option_index].name, "sele3") == 0) | 
| 1056 |  | { | 
| 276 | – | if (args_info->sele3_given) | 
| 277 | – | { | 
| 278 | – | fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 279 | – | clear_args (); | 
| 280 | – | exit (EXIT_FAILURE); | 
| 281 | – | } | 
| 282 | – | args_info->sele3_given = 1; | 
| 283 | – | args_info->sele3_arg = gengetopt_strdup (optarg); | 
| 284 | – | break; | 
| 285 | – | } | 
| 1057 |  |  | 
| 1058 | + |  | 
| 1059 | + | if (update_arg( (void *)&(args_info->sele3_arg), | 
| 1060 | + | &(args_info->sele3_orig), &(args_info->sele3_given), | 
| 1061 | + | &(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING, | 
| 1062 | + | check_ambiguity, override, 0, 0, | 
| 1063 | + | "sele3", '-', | 
| 1064 | + | additional_error)) | 
| 1065 | + | goto failure; | 
| 1066 | + |  | 
| 1067 | + | } | 
| 1068 |  | /* select reference (use and only use with --gxyz).  */ | 
| 1069 |  | else if (strcmp (long_options[option_index].name, "refsele") == 0) | 
| 1070 |  | { | 
| 1071 | < | if (args_info->refsele_given) | 
| 1072 | < | { | 
| 1073 | < | fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 1074 | < | clear_args (); | 
| 1075 | < | exit (EXIT_FAILURE); | 
| 1076 | < | } | 
| 1077 | < | args_info->refsele_given = 1; | 
| 1078 | < | args_info->refsele_arg = gengetopt_strdup (optarg); | 
| 1079 | < | break; | 
| 1071 | > |  | 
| 1072 | > |  | 
| 1073 | > | if (update_arg( (void *)&(args_info->refsele_arg), | 
| 1074 | > | &(args_info->refsele_orig), &(args_info->refsele_given), | 
| 1075 | > | &(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING, | 
| 1076 | > | check_ambiguity, override, 0, 0, | 
| 1077 | > | "refsele", '-', | 
| 1078 | > | additional_error)) | 
| 1079 | > | goto failure; | 
| 1080 | > |  | 
| 1081 |  | } | 
| 1082 | + | /* select stunt doubles for center-of-mass reference point.  */ | 
| 1083 | + | else if (strcmp (long_options[option_index].name, "comsele") == 0) | 
| 1084 | + | { | 
| 1085 |  |  | 
| 1086 | + |  | 
| 1087 | + | if (update_arg( (void *)&(args_info->comsele_arg), | 
| 1088 | + | &(args_info->comsele_orig), &(args_info->comsele_given), | 
| 1089 | + | &(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING, | 
| 1090 | + | check_ambiguity, override, 0, 0, | 
| 1091 | + | "comsele", '-', | 
| 1092 | + | additional_error)) | 
| 1093 | + | goto failure; | 
| 1094 | + |  | 
| 1095 | + | } | 
| 1096 |  | /* molecule name.  */ | 
| 1097 |  | else if (strcmp (long_options[option_index].name, "molname") == 0) | 
| 1098 |  | { | 
| 304 | – | if (args_info->molname_given) | 
| 305 | – | { | 
| 306 | – | fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 307 | – | clear_args (); | 
| 308 | – | exit (EXIT_FAILURE); | 
| 309 | – | } | 
| 310 | – | args_info->molname_given = 1; | 
| 311 | – | args_info->molname_arg = gengetopt_strdup (optarg); | 
| 312 | – | break; | 
| 313 | – | } | 
| 1099 |  |  | 
| 1100 | < | /* begin interanl index.  */ | 
| 1100 | > |  | 
| 1101 | > | if (update_arg( (void *)&(args_info->molname_arg), | 
| 1102 | > | &(args_info->molname_orig), &(args_info->molname_given), | 
| 1103 | > | &(local_args_info.molname_given), optarg, 0, 0, ARG_STRING, | 
| 1104 | > | check_ambiguity, override, 0, 0, | 
| 1105 | > | "molname", '-', | 
| 1106 | > | additional_error)) | 
| 1107 | > | goto failure; | 
| 1108 | > |  | 
| 1109 | > | } | 
| 1110 | > | /* begin internal index.  */ | 
| 1111 |  | else if (strcmp (long_options[option_index].name, "begin") == 0) | 
| 1112 |  | { | 
| 318 | – | if (args_info->begin_given) | 
| 319 | – | { | 
| 320 | – | fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 321 | – | clear_args (); | 
| 322 | – | exit (EXIT_FAILURE); | 
| 323 | – | } | 
| 324 | – | args_info->begin_given = 1; | 
| 325 | – | args_info->begin_arg = strtol (optarg,&stop_char,0); | 
| 326 | – | break; | 
| 327 | – | } | 
| 1113 |  |  | 
| 1114 | + |  | 
| 1115 | + | if (update_arg( (void *)&(args_info->begin_arg), | 
| 1116 | + | &(args_info->begin_orig), &(args_info->begin_given), | 
| 1117 | + | &(local_args_info.begin_given), optarg, 0, 0, ARG_INT, | 
| 1118 | + | check_ambiguity, override, 0, 0, | 
| 1119 | + | "begin", '-', | 
| 1120 | + | additional_error)) | 
| 1121 | + | goto failure; | 
| 1122 | + |  | 
| 1123 | + | } | 
| 1124 |  | /* end internal index.  */ | 
| 1125 |  | else if (strcmp (long_options[option_index].name, "end") == 0) | 
| 1126 |  | { | 
| 1127 | < | if (args_info->end_given) | 
| 1128 | < | { | 
| 1129 | < | fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 1130 | < | clear_args (); | 
| 1131 | < | exit (EXIT_FAILURE); | 
| 1132 | < | } | 
| 1133 | < | args_info->end_given = 1; | 
| 1134 | < | args_info->end_arg = strtol (optarg,&stop_char,0); | 
| 1135 | < | break; | 
| 1127 | > |  | 
| 1128 | > |  | 
| 1129 | > | if (update_arg( (void *)&(args_info->end_arg), | 
| 1130 | > | &(args_info->end_orig), &(args_info->end_given), | 
| 1131 | > | &(local_args_info.end_given), optarg, 0, 0, ARG_INT, | 
| 1132 | > | check_ambiguity, override, 0, 0, | 
| 1133 | > | "end", '-', | 
| 1134 | > | additional_error)) | 
| 1135 | > | goto failure; | 
| 1136 | > |  | 
| 1137 |  | } | 
| 1138 | + | /* nanoparticle radius.  */ | 
| 1139 | + | else if (strcmp (long_options[option_index].name, "radius") == 0) | 
| 1140 | + | { | 
| 1141 |  |  | 
| 1142 | < | /* g(r).  */ | 
| 1143 | < | else if (strcmp (long_options[option_index].name, "gofr") == 0) | 
| 1142 | > |  | 
| 1143 | > | if (update_arg( (void *)&(args_info->radius_arg), | 
| 1144 | > | &(args_info->radius_orig), &(args_info->radius_given), | 
| 1145 | > | &(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE, | 
| 1146 | > | check_ambiguity, override, 0, 0, | 
| 1147 | > | "radius", '-', | 
| 1148 | > | additional_error)) | 
| 1149 | > | goto failure; | 
| 1150 | > |  | 
| 1151 | > | } | 
| 1152 | > | /* bond order parameter (--rcut must be specified).  */ | 
| 1153 | > | else if (strcmp (long_options[option_index].name, "bo") == 0) | 
| 1154 |  | { | 
| 346 | – | if (args_info->gofr_given) | 
| 347 | – | { | 
| 348 | – | fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 349 | – | clear_args (); | 
| 350 | – | exit (EXIT_FAILURE); | 
| 351 | – | } | 
| 352 | – | args_info->gofr_given = 1; staticProps_group_counter += 1; | 
| 1155 |  |  | 
| 1156 | < | break; | 
| 1156 | > | if (args_info->staticProps_group_counter && override) | 
| 1157 | > | reset_group_staticProps (args_info); | 
| 1158 | > | args_info->staticProps_group_counter += 1; | 
| 1159 | > |  | 
| 1160 | > | if (update_arg( 0 , | 
| 1161 | > | 0 , &(args_info->bo_given), | 
| 1162 | > | &(local_args_info.bo_given), optarg, 0, 0, ARG_NO, | 
| 1163 | > | check_ambiguity, override, 0, 0, | 
| 1164 | > | "bo", '-', | 
| 1165 | > | additional_error)) | 
| 1166 | > | goto failure; | 
| 1167 | > |  | 
| 1168 |  | } | 
| 1169 | + | /* bond order parameter as a function of radius (--rcut must be specified).  */ | 
| 1170 | + | else if (strcmp (long_options[option_index].name, "bor") == 0) | 
| 1171 | + | { | 
| 1172 |  |  | 
| 1173 | + | if (args_info->staticProps_group_counter && override) | 
| 1174 | + | reset_group_staticProps (args_info); | 
| 1175 | + | args_info->staticProps_group_counter += 1; | 
| 1176 | + |  | 
| 1177 | + | if (update_arg( 0 , | 
| 1178 | + | 0 , &(args_info->bor_given), | 
| 1179 | + | &(local_args_info.bor_given), optarg, 0, 0, ARG_NO, | 
| 1180 | + | check_ambiguity, override, 0, 0, | 
| 1181 | + | "bor", '-', | 
| 1182 | + | additional_error)) | 
| 1183 | + | goto failure; | 
| 1184 | + |  | 
| 1185 | + | } | 
| 1186 | + | /* N(theta) bond angle density within (--rcut must be specified).  */ | 
| 1187 | + | else if (strcmp (long_options[option_index].name, "bad") == 0) | 
| 1188 | + | { | 
| 1189 | + |  | 
| 1190 | + | if (args_info->staticProps_group_counter && override) | 
| 1191 | + | reset_group_staticProps (args_info); | 
| 1192 | + | args_info->staticProps_group_counter += 1; | 
| 1193 | + |  | 
| 1194 | + | if (update_arg( 0 , | 
| 1195 | + | 0 , &(args_info->bad_given), | 
| 1196 | + | &(local_args_info.bad_given), optarg, 0, 0, ARG_NO, | 
| 1197 | + | check_ambiguity, override, 0, 0, | 
| 1198 | + | "bad", '-', | 
| 1199 | + | additional_error)) | 
| 1200 | + | goto failure; | 
| 1201 | + |  | 
| 1202 | + | } | 
| 1203 | + | /* g(z).  */ | 
| 1204 | + | else if (strcmp (long_options[option_index].name, "gofz") == 0) | 
| 1205 | + | { | 
| 1206 | + |  | 
| 1207 | + | if (args_info->staticProps_group_counter && override) | 
| 1208 | + | reset_group_staticProps (args_info); | 
| 1209 | + | args_info->staticProps_group_counter += 1; | 
| 1210 | + |  | 
| 1211 | + | if (update_arg( 0 , | 
| 1212 | + | 0 , &(args_info->gofz_given), | 
| 1213 | + | &(local_args_info.gofz_given), optarg, 0, 0, ARG_NO, | 
| 1214 | + | check_ambiguity, override, 0, 0, | 
| 1215 | + | "gofz", '-', | 
| 1216 | + | additional_error)) | 
| 1217 | + | goto failure; | 
| 1218 | + |  | 
| 1219 | + | } | 
| 1220 |  | /* g(r, cos(theta)).  */ | 
| 1221 |  | else if (strcmp (long_options[option_index].name, "r_theta") == 0) | 
| 1222 |  | { | 
| 360 | – | if (args_info->r_theta_given) | 
| 361 | – | { | 
| 362 | – | fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 363 | – | clear_args (); | 
| 364 | – | exit (EXIT_FAILURE); | 
| 365 | – | } | 
| 366 | – | args_info->r_theta_given = 1; staticProps_group_counter += 1; | 
| 1223 |  |  | 
| 1224 | < | break; | 
| 1225 | < | } | 
| 1224 | > | if (args_info->staticProps_group_counter && override) | 
| 1225 | > | reset_group_staticProps (args_info); | 
| 1226 | > | args_info->staticProps_group_counter += 1; | 
| 1227 |  |  | 
| 1228 | + | if (update_arg( 0 , | 
| 1229 | + | 0 , &(args_info->r_theta_given), | 
| 1230 | + | &(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO, | 
| 1231 | + | check_ambiguity, override, 0, 0, | 
| 1232 | + | "r_theta", '-', | 
| 1233 | + | additional_error)) | 
| 1234 | + | goto failure; | 
| 1235 | + |  | 
| 1236 | + | } | 
| 1237 |  | /* g(r, cos(omega)).  */ | 
| 1238 |  | else if (strcmp (long_options[option_index].name, "r_omega") == 0) | 
| 1239 |  | { | 
| 374 | – | if (args_info->r_omega_given) | 
| 375 | – | { | 
| 376 | – | fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 377 | – | clear_args (); | 
| 378 | – | exit (EXIT_FAILURE); | 
| 379 | – | } | 
| 380 | – | args_info->r_omega_given = 1; staticProps_group_counter += 1; | 
| 1240 |  |  | 
| 1241 | < | break; | 
| 1241 | > | if (args_info->staticProps_group_counter && override) | 
| 1242 | > | reset_group_staticProps (args_info); | 
| 1243 | > | args_info->staticProps_group_counter += 1; | 
| 1244 | > |  | 
| 1245 | > | if (update_arg( 0 , | 
| 1246 | > | 0 , &(args_info->r_omega_given), | 
| 1247 | > | &(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO, | 
| 1248 | > | check_ambiguity, override, 0, 0, | 
| 1249 | > | "r_omega", '-', | 
| 1250 | > | additional_error)) | 
| 1251 | > | goto failure; | 
| 1252 | > |  | 
| 1253 |  | } | 
| 1254 | + | /* g(r, z).  */ | 
| 1255 | + | else if (strcmp (long_options[option_index].name, "r_z") == 0) | 
| 1256 | + | { | 
| 1257 |  |  | 
| 1258 | + | if (args_info->staticProps_group_counter && override) | 
| 1259 | + | reset_group_staticProps (args_info); | 
| 1260 | + | args_info->staticProps_group_counter += 1; | 
| 1261 | + |  | 
| 1262 | + | if (update_arg( 0 , | 
| 1263 | + | 0 , &(args_info->r_z_given), | 
| 1264 | + | &(local_args_info.r_z_given), optarg, 0, 0, ARG_NO, | 
| 1265 | + | check_ambiguity, override, 0, 0, | 
| 1266 | + | "r_z", '-', | 
| 1267 | + | additional_error)) | 
| 1268 | + | goto failure; | 
| 1269 | + |  | 
| 1270 | + | } | 
| 1271 |  | /* g(cos(theta), cos(omega)).  */ | 
| 1272 |  | else if (strcmp (long_options[option_index].name, "theta_omega") == 0) | 
| 1273 |  | { | 
| 388 | – | if (args_info->theta_omega_given) | 
| 389 | – | { | 
| 390 | – | fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 391 | – | clear_args (); | 
| 392 | – | exit (EXIT_FAILURE); | 
| 393 | – | } | 
| 394 | – | args_info->theta_omega_given = 1; staticProps_group_counter += 1; | 
| 1274 |  |  | 
| 1275 | < | break; | 
| 1276 | < | } | 
| 1275 | > | if (args_info->staticProps_group_counter && override) | 
| 1276 | > | reset_group_staticProps (args_info); | 
| 1277 | > | args_info->staticProps_group_counter += 1; | 
| 1278 |  |  | 
| 1279 | + | if (update_arg( 0 , | 
| 1280 | + | 0 , &(args_info->theta_omega_given), | 
| 1281 | + | &(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO, | 
| 1282 | + | check_ambiguity, override, 0, 0, | 
| 1283 | + | "theta_omega", '-', | 
| 1284 | + | additional_error)) | 
| 1285 | + | goto failure; | 
| 1286 | + |  | 
| 1287 | + | } | 
| 1288 |  | /* g(x, y, z).  */ | 
| 1289 |  | else if (strcmp (long_options[option_index].name, "gxyz") == 0) | 
| 1290 |  | { | 
| 402 | – | if (args_info->gxyz_given) | 
| 403 | – | { | 
| 404 | – | fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 405 | – | clear_args (); | 
| 406 | – | exit (EXIT_FAILURE); | 
| 407 | – | } | 
| 408 | – | args_info->gxyz_given = 1; staticProps_group_counter += 1; | 
| 1291 |  |  | 
| 1292 | < | break; | 
| 1292 | > | if (args_info->staticProps_group_counter && override) | 
| 1293 | > | reset_group_staticProps (args_info); | 
| 1294 | > | args_info->staticProps_group_counter += 1; | 
| 1295 | > |  | 
| 1296 | > | if (update_arg( 0 , | 
| 1297 | > | 0 , &(args_info->gxyz_given), | 
| 1298 | > | &(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO, | 
| 1299 | > | check_ambiguity, override, 0, 0, | 
| 1300 | > | "gxyz", '-', | 
| 1301 | > | additional_error)) | 
| 1302 | > | goto failure; | 
| 1303 | > |  | 
| 1304 |  | } | 
| 1305 | + | /* rp2 order parameter (--sele1 and --sele2 must be specified).  */ | 
| 1306 | + | else if (strcmp (long_options[option_index].name, "rp2") == 0) | 
| 1307 | + | { | 
| 1308 |  |  | 
| 1309 | < | /* p2 order parameter (--sele1 and --sele2 must be specified).  */ | 
| 1310 | < | else if (strcmp (long_options[option_index].name, "p2") == 0) | 
| 1309 | > | if (args_info->staticProps_group_counter && override) | 
| 1310 | > | reset_group_staticProps (args_info); | 
| 1311 | > | args_info->staticProps_group_counter += 1; | 
| 1312 | > |  | 
| 1313 | > | if (update_arg( 0 , | 
| 1314 | > | 0 , &(args_info->rp2_given), | 
| 1315 | > | &(local_args_info.rp2_given), optarg, 0, 0, ARG_NO, | 
| 1316 | > | check_ambiguity, override, 0, 0, | 
| 1317 | > | "rp2", '-', | 
| 1318 | > | additional_error)) | 
| 1319 | > | goto failure; | 
| 1320 | > |  | 
| 1321 | > | } | 
| 1322 | > | /* slab density.  */ | 
| 1323 | > | else if (strcmp (long_options[option_index].name, "slab_density") == 0) | 
| 1324 |  | { | 
| 416 | – | if (args_info->p2_given) | 
| 417 | – | { | 
| 418 | – | fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 419 | – | clear_args (); | 
| 420 | – | exit (EXIT_FAILURE); | 
| 421 | – | } | 
| 422 | – | args_info->p2_given = 1; staticProps_group_counter += 1; | 
| 1325 |  |  | 
| 1326 | < | break; | 
| 1326 | > | if (args_info->staticProps_group_counter && override) | 
| 1327 | > | reset_group_staticProps (args_info); | 
| 1328 | > | args_info->staticProps_group_counter += 1; | 
| 1329 | > |  | 
| 1330 | > | if (update_arg( 0 , | 
| 1331 | > | 0 , &(args_info->slab_density_given), | 
| 1332 | > | &(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO, | 
| 1333 | > | check_ambiguity, override, 0, 0, | 
| 1334 | > | "slab_density", '-', | 
| 1335 | > | additional_error)) | 
| 1336 | > | goto failure; | 
| 1337 | > |  | 
| 1338 |  | } | 
| 1339 | + | /* p(cos(theta)).  */ | 
| 1340 | + | else if (strcmp (long_options[option_index].name, "p_angle") == 0) | 
| 1341 | + | { | 
| 1342 |  |  | 
| 1343 | < | /* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */ | 
| 1344 | < | else if (strcmp (long_options[option_index].name, "scd") == 0) | 
| 1343 | > | if (args_info->staticProps_group_counter && override) | 
| 1344 | > | reset_group_staticProps (args_info); | 
| 1345 | > | args_info->staticProps_group_counter += 1; | 
| 1346 | > |  | 
| 1347 | > | if (update_arg( 0 , | 
| 1348 | > | 0 , &(args_info->p_angle_given), | 
| 1349 | > | &(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO, | 
| 1350 | > | check_ambiguity, override, 0, 0, | 
| 1351 | > | "p_angle", '-', | 
| 1352 | > | additional_error)) | 
| 1353 | > | goto failure; | 
| 1354 | > |  | 
| 1355 | > | } | 
| 1356 | > | /* hxy.  */ | 
| 1357 | > | else if (strcmp (long_options[option_index].name, "hxy") == 0) | 
| 1358 |  | { | 
| 430 | – | if (args_info->scd_given) | 
| 431 | – | { | 
| 432 | – | fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE); | 
| 433 | – | clear_args (); | 
| 434 | – | exit (EXIT_FAILURE); | 
| 435 | – | } | 
| 436 | – | args_info->scd_given = 1; staticProps_group_counter += 1; | 
| 1359 |  |  | 
| 1360 | < | break; | 
| 1360 | > | if (args_info->staticProps_group_counter && override) | 
| 1361 | > | reset_group_staticProps (args_info); | 
| 1362 | > | args_info->staticProps_group_counter += 1; | 
| 1363 | > |  | 
| 1364 | > | if (update_arg( 0 , | 
| 1365 | > | 0 , &(args_info->hxy_given), | 
| 1366 | > | &(local_args_info.hxy_given), optarg, 0, 0, ARG_NO, | 
| 1367 | > | check_ambiguity, override, 0, 0, | 
| 1368 | > | "hxy", '-', | 
| 1369 | > | additional_error)) | 
| 1370 | > | goto failure; | 
| 1371 | > |  | 
| 1372 |  | } | 
| 1373 | + | /* rho of R.  */ | 
| 1374 | + | else if (strcmp (long_options[option_index].name, "rho_r") == 0) | 
| 1375 | + | { | 
| 1376 |  |  | 
| 1377 | < |  | 
| 1377 | > | if (args_info->staticProps_group_counter && override) | 
| 1378 | > | reset_group_staticProps (args_info); | 
| 1379 | > | args_info->staticProps_group_counter += 1; | 
| 1380 | > |  | 
| 1381 | > | if (update_arg( 0 , | 
| 1382 | > | 0 , &(args_info->rho_r_given), | 
| 1383 | > | &(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO, | 
| 1384 | > | check_ambiguity, override, 0, 0, | 
| 1385 | > | "rho_r", '-', | 
| 1386 | > | additional_error)) | 
| 1387 | > | goto failure; | 
| 1388 | > |  | 
| 1389 | > | } | 
| 1390 | > | /* hull volume of nanoparticle.  */ | 
| 1391 | > | else if (strcmp (long_options[option_index].name, "hullvol") == 0) | 
| 1392 | > | { | 
| 1393 | > |  | 
| 1394 | > | if (args_info->staticProps_group_counter && override) | 
| 1395 | > | reset_group_staticProps (args_info); | 
| 1396 | > | args_info->staticProps_group_counter += 1; | 
| 1397 | > |  | 
| 1398 | > | if (update_arg( 0 , | 
| 1399 | > | 0 , &(args_info->hullvol_given), | 
| 1400 | > | &(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO, | 
| 1401 | > | check_ambiguity, override, 0, 0, | 
| 1402 | > | "hullvol", '-', | 
| 1403 | > | additional_error)) | 
| 1404 | > | goto failure; | 
| 1405 | > |  | 
| 1406 | > | } | 
| 1407 | > |  | 
| 1408 | > | break; | 
| 1409 |  | case '?':       /* Invalid option.  */ | 
| 1410 |  | /* `getopt_long' already printed an error message.  */ | 
| 1411 | < | exit (EXIT_FAILURE); | 
| 1411 | > | goto failure; | 
| 1412 |  |  | 
| 1413 |  | default:        /* bug: option not considered.  */ | 
| 1414 | < | fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c); | 
| 1414 | > | fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : "")); | 
| 1415 |  | abort (); | 
| 1416 |  | } /* switch */ | 
| 1417 |  | } /* while */ | 
| 1418 |  |  | 
| 1419 | < | if ( staticProps_group_counter != 1) | 
| 1419 | > | if (args_info->staticProps_group_counter > 1) | 
| 1420 |  | { | 
| 1421 | < | fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter); | 
| 1422 | < | missing_required_options = 1; | 
| 1421 | > | fprintf (stderr, "%s: %d options of group staticProps were given. One is required.%s\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : "")); | 
| 1422 | > | error = 1; | 
| 1423 |  | } | 
| 1424 |  |  | 
| 1425 |  |  | 
| 1426 | < | if (! args_info->input_given) | 
| 1426 | > |  | 
| 1427 | > | if (check_required) | 
| 1428 |  | { | 
| 1429 | < | fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE); | 
| 462 | < | missing_required_options = 1; | 
| 1429 | > | error += cmdline_parser_required2 (args_info, argv[0], additional_error); | 
| 1430 |  | } | 
| 464 | – | if ( missing_required_options ) | 
| 465 | – | exit (EXIT_FAILURE); | 
| 1431 |  |  | 
| 1432 | + | cmdline_parser_release (&local_args_info); | 
| 1433 | + |  | 
| 1434 | + | if ( error ) | 
| 1435 | + | return (EXIT_FAILURE); | 
| 1436 | + |  | 
| 1437 | + | if (optind < argc) | 
| 1438 | + | { | 
| 1439 | + | int i = 0 ; | 
| 1440 | + | int found_prog_name = 0; | 
| 1441 | + | /* whether program name, i.e., argv[0], is in the remaining args | 
| 1442 | + | (this may happen with some implementations of getopt, | 
| 1443 | + | but surely not with the one included by gengetopt) */ | 
| 1444 | + |  | 
| 1445 | + | i = optind; | 
| 1446 | + | while (i < argc) | 
| 1447 | + | if (argv[i++] == argv[0]) { | 
| 1448 | + | found_prog_name = 1; | 
| 1449 | + | break; | 
| 1450 | + | } | 
| 1451 | + | i = 0; | 
| 1452 | + |  | 
| 1453 | + | args_info->inputs_num = argc - optind - found_prog_name; | 
| 1454 | + | args_info->inputs = | 
| 1455 | + | (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ; | 
| 1456 | + | while (optind < argc) | 
| 1457 | + | if (argv[optind++] != argv[0]) | 
| 1458 | + | args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ; | 
| 1459 | + | } | 
| 1460 | + |  | 
| 1461 |  | return 0; | 
| 1462 | + |  | 
| 1463 | + | failure: | 
| 1464 | + |  | 
| 1465 | + | cmdline_parser_release (&local_args_info); | 
| 1466 | + | return (EXIT_FAILURE); | 
| 1467 |  | } |